What are the expression values for each gene based on?
All the data displayed on SpermBase are average normalized expression values. Small RNA gene expression is given as reads per hundred thousand aligned reads (RPK) and large RNA gene expression is given as reads per kilobase per million aligned reads (RPKM).
Where can I download the sequencing data used for SpermBase?
The sequencing data used for SpermBase can be downloaded from GEO.
What sequencing platform(s) did you use to generate the data for SpermBase?
All sequencing was performed using the Ion Torrent suite. Mouse sperm head and human whole sperm small RNA data was generated using the Ion Personal Genome Machine and all other data was generated on the Ion Proton System.
Why are there sncRNA genes from other species in the rabbit data?
Very few miRNA and no piRNA have been annotated in rabbit, therefore, we used known human, rat, and mouse miRNA and piRNA as additional references when analyzing the rabbit sncRNA-Seq data. Novel piRNA were also predicted using the rabbit whole sperm sncRNA-Seq data via piRNApredictor. Details can be found in our publication.
For all general inquires and issues concerning SpermBase, please contact us at firstname.lastname@example.org
SpermBase was created, and is maintained, by the Wei Yan lab, located within the Center for Molecular Medicine at the University of Nevada, Reno.
Current curators of SpermBase